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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-10-04, 13:38 PDT based on data in: /scratch/st-spakpour-1/bioinformatic-pipelines-workflow/qc_results/fastqc_trimmed_25_60_15


        General Statistics

        Showing 362/362 rows and 4/5 columns.
        Sample Name% Dups% GCRead LengthM Seqs
        02-01-Li41560-CAACGTAC_R1_kneaddata_paired_1
        23.1%
        51%
        113 bp
        11.7
        02-01-Li41560-CAACGTAC_R1_kneaddata_paired_2
        16.6%
        51%
        122 bp
        11.7
        100-01-Li41380-CGTACGTA_R1_kneaddata_paired_1
        26.4%
        48%
        113 bp
        10.0
        100-01-Li41380-CGTACGTA_R1_kneaddata_paired_2
        19.0%
        48%
        122 bp
        10.0
        100-02-Li41381-AGGAACGT_R1_kneaddata_paired_1
        21.3%
        45%
        113 bp
        7.1
        100-02-Li41381-AGGAACGT_R1_kneaddata_paired_2
        17.3%
        45%
        122 bp
        7.1
        100-04-Li41382-CTAGCTAG_R1_kneaddata_paired_1
        19.2%
        50%
        113 bp
        7.8
        100-04-Li41382-CTAGCTAG_R1_kneaddata_paired_2
        14.5%
        50%
        122 bp
        7.8
        100-05-Li41383-CTCTCAGT_R1_kneaddata_paired_1
        12.3%
        47%
        113 bp
        5.1
        100-05-Li41383-CTCTCAGT_R1_kneaddata_paired_2
        10.0%
        47%
        122 bp
        5.1
        100-06-Li41384-GTACTGCA_R1_kneaddata_paired_1
        25.9%
        49%
        113 bp
        8.4
        100-06-Li41384-GTACTGCA_R1_kneaddata_paired_2
        19.1%
        49%
        122 bp
        8.4
        100-07-Li41385-CTTCCATG_R1_kneaddata_paired_1
        18.7%
        48%
        113 bp
        6.9
        100-07-Li41385-CTTCCATG_R1_kneaddata_paired_2
        13.7%
        48%
        122 bp
        6.9
        100-08-Li41386-TACGAACC_R1_kneaddata_paired_1
        22.5%
        48%
        113 bp
        8.5
        100-08-Li41386-TACGAACC_R1_kneaddata_paired_2
        15.7%
        48%
        122 bp
        8.5
        100-09-Li41387-TACCATGG_R1_kneaddata_paired_1
        22.3%
        48%
        113 bp
        6.1
        100-09-Li41387-TACCATGG_R1_kneaddata_paired_2
        16.1%
        48%
        122 bp
        6.1
        100-10-Li41388-AGCTAGCT_R1_kneaddata_paired_1
        26.6%
        51%
        113 bp
        11.0
        100-10-Li41388-AGCTAGCT_R1_kneaddata_paired_2
        18.7%
        51%
        122 bp
        11.0
        100-12-Li41389-AGGTAGGT_R1_kneaddata_paired_1
        16.4%
        46%
        113 bp
        6.5
        100-12-Li41389-AGGTAGGT_R1_kneaddata_paired_2
        13.8%
        46%
        122 bp
        6.5
        100-13-Li41390-CAGTCAGT_R1_kneaddata_paired_1
        23.0%
        48%
        113 bp
        7.8
        100-13-Li41390-CAGTCAGT_R1_kneaddata_paired_2
        17.5%
        48%
        122 bp
        7.8
        100-14-Li41391-CAAGCTTG_R1_kneaddata_paired_1
        16.7%
        49%
        113 bp
        6.4
        100-14-Li41391-CAAGCTTG_R1_kneaddata_paired_2
        11.5%
        49%
        122 bp
        6.4
        100-15-Li41392-AACCTTGG_R1_kneaddata_paired_1
        23.7%
        49%
        113 bp
        7.2
        100-15-Li41392-AACCTTGG_R1_kneaddata_paired_2
        17.4%
        49%
        122 bp
        7.2
        100-17-Li41393-ATCGTAGC_R1_kneaddata_paired_1
        16.3%
        51%
        113 bp
        4.5
        100-17-Li41393-ATCGTAGC_R1_kneaddata_paired_2
        12.6%
        50%
        122 bp
        4.5
        100-18-Li41394-CACTAGAC_R1_kneaddata_paired_1
        16.1%
        50%
        113 bp
        6.3
        100-18-Li41394-CACTAGAC_R1_kneaddata_paired_2
        12.0%
        50%
        122 bp
        6.3
        100-19-Li41395-GCTTCCTA_R1_kneaddata_paired_1
        24.2%
        48%
        113 bp
        6.0
        100-19-Li41395-GCTTCCTA_R1_kneaddata_paired_2
        19.0%
        48%
        122 bp
        6.0
        100-20-Li41396-GCTTAACG_R1_kneaddata_paired_1
        25.6%
        50%
        113 bp
        7.9
        100-20-Li41396-GCTTAACG_R1_kneaddata_paired_2
        21.0%
        50%
        122 bp
        7.9
        100-21-Li41397-GTACCAAC_R1_kneaddata_paired_1
        15.3%
        47%
        113 bp
        6.8
        100-21-Li41397-GTACCAAC_R1_kneaddata_paired_2
        11.5%
        47%
        122 bp
        6.8
        100-22-Li41398-GAAGTCCT_R1_kneaddata_paired_1
        18.5%
        50%
        113 bp
        4.2
        100-22-Li41398-GAAGTCCT_R1_kneaddata_paired_2
        11.4%
        50%
        122 bp
        4.2
        100-23-Li41399-CCAATACG_R1_kneaddata_paired_1
        11.9%
        47%
        113 bp
        4.6
        100-23-Li41399-CCAATACG_R1_kneaddata_paired_2
        10.4%
        47%
        122 bp
        4.6
        100-24-Li41400-AGCTCTAG_R1_kneaddata_paired_1
        27.5%
        53%
        113 bp
        4.5
        100-24-Li41400-AGCTCTAG_R1_kneaddata_paired_2
        19.5%
        53%
        122 bp
        4.5
        100-25-Li41401-CGTAGCTA_R1_kneaddata_paired_1
        18.8%
        50%
        113 bp
        5.2
        100-25-Li41401-CGTAGCTA_R1_kneaddata_paired_2
        16.1%
        50%
        122 bp
        5.2
        100-26-Li41402-CTCTCACA_R1_kneaddata_paired_1
        15.5%
        48%
        113 bp
        4.6
        100-26-Li41402-CTCTCACA_R1_kneaddata_paired_2
        11.4%
        48%
        122 bp
        4.6
        100-27-Li41403-TGACCACA_R1_kneaddata_paired_1
        14.2%
        50%
        113 bp
        5.8
        100-27-Li41403-TGACCACA_R1_kneaddata_paired_2
        9.4%
        50%
        122 bp
        5.8
        100-28-Li41404-ATCCGGTA_R1_kneaddata_paired_1
        19.5%
        46%
        113 bp
        10.0
        100-28-Li41404-ATCCGGTA_R1_kneaddata_paired_2
        15.8%
        46%
        122 bp
        10.0
        100-29-Li41405-GACATCAC_R1_kneaddata_paired_1
        15.8%
        49%
        113 bp
        5.6
        100-29-Li41405-GACATCAC_R1_kneaddata_paired_2
        11.8%
        49%
        122 bp
        5.6
        100-30-Li41406-TCGATGGT_R1_kneaddata_paired_1
        25.9%
        49%
        113 bp
        8.6
        100-30-Li41406-TCGATGGT_R1_kneaddata_paired_2
        20.9%
        49%
        122 bp
        8.6
        100-31-Li41407-CTGTCAGA_R1_kneaddata_paired_1
        19.5%
        50%
        113 bp
        7.4
        100-31-Li41407-CTGTCAGA_R1_kneaddata_paired_2
        13.6%
        50%
        122 bp
        7.4
        100-32-Li41408-TGGTACGT_R1_kneaddata_paired_1
        22.3%
        50%
        113 bp
        7.3
        100-32-Li41408-TGGTACGT_R1_kneaddata_paired_2
        16.8%
        50%
        122 bp
        7.3
        100-33-Li41409-GATGCATC_R1_kneaddata_paired_1
        15.3%
        51%
        113 bp
        3.6
        100-33-Li41409-GATGCATC_R1_kneaddata_paired_2
        10.6%
        51%
        122 bp
        3.6
        100-34-Li41410-CTTCCAAC_R1_kneaddata_paired_1
        16.8%
        49%
        113 bp
        6.5
        100-34-Li41410-CTTCCAAC_R1_kneaddata_paired_2
        12.4%
        49%
        122 bp
        6.5
        100-35-Li41411-ACACGTGT_R1_kneaddata_paired_1
        17.4%
        48%
        113 bp
        5.9
        100-35-Li41411-ACACGTGT_R1_kneaddata_paired_2
        12.3%
        48%
        122 bp
        5.9
        200-01-Li41412-TAGGCCAT_R1_kneaddata_paired_1
        20.9%
        53%
        113 bp
        5.7
        200-01-Li41412-TAGGCCAT_R1_kneaddata_paired_2
        12.6%
        52%
        122 bp
        5.7
        200-02-Li41413-CTGTACAG_R1_kneaddata_paired_1
        24.0%
        50%
        113 bp
        4.1
        200-02-Li41413-CTGTACAG_R1_kneaddata_paired_2
        15.4%
        50%
        122 bp
        4.1
        200-03-Li41414-TCGAGTTG_R1_kneaddata_paired_1
        17.0%
        49%
        113 bp
        5.4
        200-03-Li41414-TCGAGTTG_R1_kneaddata_paired_2
        12.8%
        49%
        122 bp
        5.4
        200-04-Li41415-AAGGTTCC_R1_kneaddata_paired_1
        16.5%
        46%
        113 bp
        5.4
        200-04-Li41415-AAGGTTCC_R1_kneaddata_paired_2
        13.1%
        46%
        122 bp
        5.4
        200-05-Li41416-GCCGTATA_R1_kneaddata_paired_1
        14.2%
        47%
        113 bp
        3.3
        200-05-Li41416-GCCGTATA_R1_kneaddata_paired_2
        12.4%
        47%
        122 bp
        3.3
        200-07-Li41417-ACCTGTTC_R1_kneaddata_paired_1
        21.6%
        51%
        113 bp
        4.1
        200-07-Li41417-ACCTGTTC_R1_kneaddata_paired_2
        14.8%
        51%
        122 bp
        4.1
        200-08-Li41418-ACAGTCAC_R1_kneaddata_paired_1
        16.6%
        50%
        113 bp
        2.6
        200-08-Li41418-ACAGTCAC_R1_kneaddata_paired_2
        9.0%
        50%
        122 bp
        2.6
        200-09-Li41419-GAGTTCTG_R1_kneaddata_paired_1
        25.6%
        46%
        113 bp
        7.4
        200-09-Li41419-GAGTTCTG_R1_kneaddata_paired_2
        21.2%
        46%
        122 bp
        7.4
        200-10-Li41420-GCTACGAT_R1_kneaddata_paired_1
        23.0%
        51%
        113 bp
        8.3
        200-10-Li41420-GCTACGAT_R1_kneaddata_paired_2
        16.3%
        51%
        122 bp
        8.3
        200-11-Li41421-CTAGAGCT_R1_kneaddata_paired_1
        19.0%
        49%
        113 bp
        4.7
        200-11-Li41421-CTAGAGCT_R1_kneaddata_paired_2
        16.0%
        49%
        122 bp
        4.7
        200-12-Li41422-ACTGACTG_R1_kneaddata_paired_1
        16.0%
        45%
        113 bp
        5.3
        200-12-Li41422-ACTGACTG_R1_kneaddata_paired_2
        11.6%
        45%
        122 bp
        5.3
        200-13-Li41423-GGAAGCAT_R1_kneaddata_paired_1
        17.3%
        45%
        113 bp
        6.0
        200-13-Li41423-GGAAGCAT_R1_kneaddata_paired_2
        14.5%
        46%
        122 bp
        6.0
        200-14-Li41424-CCATATGG_R1_kneaddata_paired_1
        16.7%
        49%
        113 bp
        5.8
        200-14-Li41424-CCATATGG_R1_kneaddata_paired_2
        12.2%
        49%
        122 bp
        5.8
        200-15-Li41425-CAGTTGAC_R1_kneaddata_paired_1
        19.2%
        49%
        113 bp
        5.4
        200-15-Li41425-CAGTTGAC_R1_kneaddata_paired_2
        14.7%
        49%
        122 bp
        5.4
        200-16-Li41426-ACACGTCA_R1_kneaddata_paired_1
        21.5%
        47%
        113 bp
        4.9
        200-16-Li41426-ACACGTCA_R1_kneaddata_paired_2
        15.4%
        47%
        122 bp
        4.9
        200-17-Li41427-ACCAACGT_R1_kneaddata_paired_1
        24.1%
        48%
        113 bp
        8.5
        200-17-Li41427-ACCAACGT_R1_kneaddata_paired_2
        18.7%
        48%
        122 bp
        8.5
        200-18-Li41428-GATCAGCT_R1_kneaddata_paired_1
        22.6%
        49%
        113 bp
        7.4
        200-18-Li41428-GATCAGCT_R1_kneaddata_paired_2
        16.1%
        49%
        122 bp
        7.4
        300-01-Li41429-CGTAGCAT_R1_kneaddata_paired_1
        14.2%
        45%
        113 bp
        8.5
        300-01-Li41429-CGTAGCAT_R1_kneaddata_paired_2
        11.9%
        45%
        122 bp
        8.5
        300-02-Li41430-GTGTTGAC_R1_kneaddata_paired_1
        12.7%
        48%
        113 bp
        2.8
        300-02-Li41430-GTGTTGAC_R1_kneaddata_paired_2
        8.5%
        48%
        122 bp
        2.8
        300-03-Li41431-AGTGTCTG_R1_kneaddata_paired_1
        16.4%
        50%
        113 bp
        6.4
        300-03-Li41431-AGTGTCTG_R1_kneaddata_paired_2
        11.9%
        50%
        122 bp
        6.4
        300-04-Li41432-TGGTCATG_R1_kneaddata_paired_1
        19.1%
        50%
        113 bp
        6.7
        300-04-Li41432-TGGTCATG_R1_kneaddata_paired_2
        14.8%
        50%
        122 bp
        6.7
        300-05-Li41433-ACTGTGAC_R1_kneaddata_paired_1
        13.1%
        48%
        113 bp
        4.0
        300-05-Li41433-ACTGTGAC_R1_kneaddata_paired_2
        9.6%
        48%
        122 bp
        4.0
        300-06-Li41434-CTTGTCCA_R1_kneaddata_paired_1
        13.8%
        48%
        113 bp
        3.2
        300-06-Li41434-CTTGTCCA_R1_kneaddata_paired_2
        9.3%
        48%
        122 bp
        3.2
        300-07-Li41435-CGATCGAT_R1_kneaddata_paired_1
        24.8%
        47%
        113 bp
        11.4
        300-07-Li41435-CGATCGAT_R1_kneaddata_paired_2
        19.0%
        47%
        122 bp
        11.4
        300-08-Li41436-AACGTTGC_R1_kneaddata_paired_1
        20.3%
        49%
        113 bp
        7.6
        300-08-Li41436-AACGTTGC_R1_kneaddata_paired_2
        13.2%
        49%
        122 bp
        7.6
        300-09-Li41437-TGCACAAC_R1_kneaddata_paired_1
        15.8%
        47%
        113 bp
        7.3
        300-09-Li41437-TGCACAAC_R1_kneaddata_paired_2
        12.4%
        47%
        122 bp
        7.3
        300-10-Li41438-CTCTACAC_R1_kneaddata_paired_1
        13.2%
        49%
        113 bp
        6.2
        300-10-Li41438-CTCTACAC_R1_kneaddata_paired_2
        9.8%
        49%
        122 bp
        6.2
        300-11-Li41439-GCTATTCC_R1_kneaddata_paired_1
        13.4%
        49%
        113 bp
        5.4
        300-11-Li41439-GCTATTCC_R1_kneaddata_paired_2
        10.0%
        49%
        122 bp
        5.4
        300-12-Li41440-CCTAATCC_R1_kneaddata_paired_1
        13.2%
        48%
        113 bp
        2.9
        300-12-Li41440-CCTAATCC_R1_kneaddata_paired_2
        8.3%
        48%
        122 bp
        2.9
        300-13-Li41441-CATGCTTC_R1_kneaddata_paired_1
        18.8%
        46%
        113 bp
        5.1
        300-13-Li41441-CATGCTTC_R1_kneaddata_paired_2
        13.4%
        47%
        122 bp
        5.1
        300-14-Li41442-TGACGTGT_R1_kneaddata_paired_1
        12.2%
        48%
        113 bp
        4.6
        300-14-Li41442-TGACGTGT_R1_kneaddata_paired_2
        9.3%
        48%
        122 bp
        4.6
        300-15-Li41443-ACCACATG_R1_kneaddata_paired_1
        28.3%
        47%
        113 bp
        12.6
        300-15-Li41443-ACCACATG_R1_kneaddata_paired_2
        23.1%
        47%
        122 bp
        12.6
        300-16-Li41444-GACTTCAG_R1_kneaddata_paired_1
        22.0%
        52%
        113 bp
        6.4
        300-16-Li41444-GACTTCAG_R1_kneaddata_paired_2
        13.6%
        51%
        122 bp
        6.4
        300-17-Li41445-ACCAAGGA_R1_kneaddata_paired_1
        16.5%
        50%
        113 bp
        6.1
        300-17-Li41445-ACCAAGGA_R1_kneaddata_paired_2
        11.9%
        50%
        122 bp
        6.1
        300-18-Li41446-GCCGTTAA_R1_kneaddata_paired_1
        15.4%
        48%
        113 bp
        6.0
        300-18-Li41446-GCCGTTAA_R1_kneaddata_paired_2
        12.1%
        48%
        122 bp
        6.0
        300-19-Li41447-TGACTGAC_R1_kneaddata_paired_1
        9.0%
        48%
        113 bp
        2.9
        300-19-Li41447-TGACTGAC_R1_kneaddata_paired_2
        7.7%
        48%
        122 bp
        2.9
        300-20-Li41448-TGGTGTAC_R1_kneaddata_paired_1
        15.0%
        48%
        113 bp
        4.6
        300-20-Li41448-TGGTGTAC_R1_kneaddata_paired_2
        10.1%
        48%
        122 bp
        4.6
        300-21-Li41449-GTACAGCT_R1_kneaddata_paired_1
        26.1%
        47%
        113 bp
        7.0
        300-21-Li41449-GTACAGCT_R1_kneaddata_paired_2
        17.6%
        47%
        122 bp
        7.0
        300-22-Li41450-GGTTCCAA_R1_kneaddata_paired_1
        18.3%
        48%
        113 bp
        8.0
        300-22-Li41450-GGTTCCAA_R1_kneaddata_paired_2
        14.1%
        48%
        122 bp
        8.0
        300-23-Li41451-GAGACACA_R1_kneaddata_paired_1
        28.4%
        49%
        113 bp
        9.2
        300-23-Li41451-GAGACACA_R1_kneaddata_paired_2
        22.0%
        49%
        122 bp
        9.2
        300-24-Li41452-GAGTTCAC_R1_kneaddata_paired_1
        19.1%
        47%
        113 bp
        8.1
        300-24-Li41452-GAGTTCAC_R1_kneaddata_paired_2
        14.9%
        47%
        122 bp
        8.1
        300-25-Li41453-GCGCTATA_R1_kneaddata_paired_1
        21.2%
        49%
        113 bp
        7.0
        300-25-Li41453-GCGCTATA_R1_kneaddata_paired_2
        16.6%
        49%
        122 bp
        7.0
        300-26-Li41454-GTGAACAG_R1_kneaddata_paired_1
        23.3%
        49%
        113 bp
        11.2
        300-26-Li41454-GTGAACAG_R1_kneaddata_paired_2
        18.1%
        49%
        122 bp
        11.2
        300-27-Li41455-TGCACTAG_R1_kneaddata_paired_1
        11.5%
        47%
        113 bp
        4.3
        300-27-Li41455-TGCACTAG_R1_kneaddata_paired_2
        10.0%
        47%
        122 bp
        4.3
        300-28-Li41456-AACCGGTT_R1_kneaddata_paired_1
        15.3%
        47%
        113 bp
        6.0
        300-28-Li41456-AACCGGTT_R1_kneaddata_paired_2
        11.3%
        47%
        122 bp
        6.0
        300-29-Li41457-ATCCTAGG_R1_kneaddata_paired_1
        19.5%
        48%
        113 bp
        8.1
        300-29-Li41457-ATCCTAGG_R1_kneaddata_paired_2
        15.6%
        48%
        122 bp
        8.1
        300-30-Li41458-CAACCTAG_R1_kneaddata_paired_1
        18.0%
        48%
        113 bp
        5.5
        300-30-Li41458-CAACCTAG_R1_kneaddata_paired_2
        13.0%
        48%
        122 bp
        5.5
        300-31-Li41459-AGTGGTCT_R1_kneaddata_paired_1
        15.7%
        46%
        113 bp
        7.5
        300-31-Li41459-AGTGGTCT_R1_kneaddata_paired_2
        11.7%
        46%
        122 bp
        7.5
        300-32-Li41460-GGATTAGG_R1_kneaddata_paired_1
        20.9%
        48%
        113 bp
        9.1
        300-32-Li41460-GGATTAGG_R1_kneaddata_paired_2
        16.7%
        48%
        122 bp
        9.1
        300-33-Li41461-GAACCATC_R1_kneaddata_paired_1
        19.2%
        49%
        113 bp
        8.8
        300-33-Li41461-GAACCATC_R1_kneaddata_paired_2
        13.4%
        49%
        122 bp
        8.8
        300-34-Li41462-ATGCATGC_R1_kneaddata_paired_1
        18.1%
        51%
        113 bp
        8.5
        300-34-Li41462-ATGCATGC_R1_kneaddata_paired_2
        12.9%
        50%
        122 bp
        8.5
        300-35-Li41463-GATCCTAG_R1_kneaddata_paired_1
        13.9%
        51%
        113 bp
        3.2
        300-35-Li41463-GATCCTAG_R1_kneaddata_paired_2
        8.4%
        51%
        122 bp
        3.2
        300-36-Li41464-CAACGTAC_R1_kneaddata_paired_1
        14.8%
        48%
        113 bp
        5.9
        300-36-Li41464-CAACGTAC_R1_kneaddata_paired_2
        10.9%
        48%
        122 bp
        5.9
        300-37-Li41465-GAAGCTTC_R1_kneaddata_paired_1
        21.0%
        51%
        113 bp
        4.1
        300-37-Li41465-GAAGCTTC_R1_kneaddata_paired_2
        13.2%
        51%
        122 bp
        4.1
        300-38-Li41466-TAGCTACG_R1_kneaddata_paired_1
        19.2%
        51%
        113 bp
        5.0
        300-38-Li41466-TAGCTACG_R1_kneaddata_paired_2
        12.1%
        51%
        122 bp
        5.0
        300-39-Li41467-GAACTGCT_R1_kneaddata_paired_1
        28.2%
        46%
        113 bp
        10.6
        300-39-Li41467-GAACTGCT_R1_kneaddata_paired_2
        21.2%
        46%
        122 bp
        10.6
        300-40-Li41468-TGGTCTAG_R1_kneaddata_paired_1
        18.6%
        49%
        113 bp
        7.5
        300-40-Li41468-TGGTCTAG_R1_kneaddata_paired_2
        13.4%
        49%
        122 bp
        7.5
        300-41-Li41469-CTACCATC_R1_kneaddata_paired_1
        26.2%
        48%
        113 bp
        8.5
        300-41-Li41469-CTACCATC_R1_kneaddata_paired_2
        19.3%
        48%
        122 bp
        8.5
        400-01-Li41470-TCCAAGGT_R1_kneaddata_paired_1
        24.2%
        50%
        113 bp
        9.4
        400-01-Li41470-TCCAAGGT_R1_kneaddata_paired_2
        17.8%
        50%
        122 bp
        9.4
        400-02-Li41471-CTCATGAG_R1_kneaddata_paired_1
        14.7%
        49%
        113 bp
        4.5
        400-02-Li41471-CTCATGAG_R1_kneaddata_paired_2
        10.6%
        49%
        122 bp
        4.5
        400-03-Li41472-GAGACAGT_R1_kneaddata_paired_1
        15.0%
        47%
        113 bp
        4.5
        400-03-Li41472-GAGACAGT_R1_kneaddata_paired_2
        12.0%
        47%
        122 bp
        4.5
        400-04-Li41473-GTGTCACA_R1_kneaddata_paired_1
        19.4%
        47%
        113 bp
        5.3
        400-04-Li41473-GTGTCACA_R1_kneaddata_paired_2
        13.6%
        47%
        122 bp
        5.3
        400-05-Li41474-GACATCTG_R1_kneaddata_paired_1
        17.9%
        50%
        113 bp
        7.9
        400-05-Li41474-GACATCTG_R1_kneaddata_paired_2
        12.7%
        50%
        122 bp
        7.9
        400-06-Li41475-CACATGTG_R1_kneaddata_paired_1
        19.8%
        47%
        113 bp
        3.8
        400-06-Li41475-CACATGTG_R1_kneaddata_paired_2
        12.4%
        47%
        122 bp
        3.8
        400-07-Li41476-CGTACGTA_R1_kneaddata_paired_1
        22.4%
        47%
        113 bp
        12.4
        400-07-Li41476-CGTACGTA_R1_kneaddata_paired_2
        17.1%
        47%
        122 bp
        12.4
        400-08-Li41477-AGGAACGT_R1_kneaddata_paired_1
        20.7%
        48%
        113 bp
        10.9
        400-08-Li41477-AGGAACGT_R1_kneaddata_paired_2
        16.6%
        48%
        122 bp
        10.9
        400-09-Li41478-CTAGCTAG_R1_kneaddata_paired_1
        24.0%
        48%
        113 bp
        11.5
        400-09-Li41478-CTAGCTAG_R1_kneaddata_paired_2
        19.6%
        48%
        122 bp
        11.5
        400-10-Li41479-CTCTCAGT_R1_kneaddata_paired_1
        18.4%
        46%
        113 bp
        11.7
        400-10-Li41479-CTCTCAGT_R1_kneaddata_paired_2
        15.5%
        46%
        122 bp
        11.7
        400-11-Li41480-GTACTGCA_R1_kneaddata_paired_1
        26.3%
        50%
        113 bp
        15.7
        400-11-Li41480-GTACTGCA_R1_kneaddata_paired_2
        18.8%
        50%
        122 bp
        15.7
        400-12-Li41481-CTTCCATG_R1_kneaddata_paired_1
        25.0%
        49%
        113 bp
        11.3
        400-12-Li41481-CTTCCATG_R1_kneaddata_paired_2
        18.4%
        48%
        122 bp
        11.3
        400-13-Li41482-TACGAACC_R1_kneaddata_paired_1
        22.3%
        49%
        113 bp
        10.9
        400-13-Li41482-TACGAACC_R1_kneaddata_paired_2
        16.1%
        49%
        122 bp
        10.9
        400-14-Li41483-TACCATGG_R1_kneaddata_paired_1
        26.0%
        51%
        113 bp
        13.3
        400-14-Li41483-TACCATGG_R1_kneaddata_paired_2
        17.7%
        50%
        122 bp
        13.3
        400-15-Li41484-AGCTAGCT_R1_kneaddata_paired_1
        25.5%
        50%
        113 bp
        13.8
        400-15-Li41484-AGCTAGCT_R1_kneaddata_paired_2
        17.4%
        50%
        122 bp
        13.8
        400-16-Li41485-AGGTAGGT_R1_kneaddata_paired_1
        30.0%
        49%
        113 bp
        11.0
        400-16-Li41485-AGGTAGGT_R1_kneaddata_paired_2
        25.3%
        49%
        123 bp
        11.0
        400-18-Li41486-CAGTCAGT_R1_kneaddata_paired_1
        25.3%
        49%
        113 bp
        13.6
        400-18-Li41486-CAGTCAGT_R1_kneaddata_paired_2
        18.8%
        48%
        122 bp
        13.6
        400-19-Li41487-CAAGCTTG_R1_kneaddata_paired_1
        25.9%
        51%
        113 bp
        14.3
        400-19-Li41487-CAAGCTTG_R1_kneaddata_paired_2
        18.3%
        51%
        122 bp
        14.3
        400-20-Li41488-AACCTTGG_R1_kneaddata_paired_1
        22.2%
        48%
        113 bp
        9.9
        400-20-Li41488-AACCTTGG_R1_kneaddata_paired_2
        16.5%
        48%
        122 bp
        9.9
        400-21-Li41489-ATCGTAGC_R1_kneaddata_paired_1
        24.2%
        49%
        113 bp
        12.3
        400-21-Li41489-ATCGTAGC_R1_kneaddata_paired_2
        17.9%
        49%
        122 bp
        12.3
        400-22-Li41490-CACTAGAC_R1_kneaddata_paired_1
        28.0%
        48%
        113 bp
        12.8
        400-22-Li41490-CACTAGAC_R1_kneaddata_paired_2
        20.7%
        48%
        122 bp
        12.8
        400-23-Li41491-GCTTCCTA_R1_kneaddata_paired_1
        24.1%
        48%
        113 bp
        17.2
        400-23-Li41491-GCTTCCTA_R1_kneaddata_paired_2
        17.9%
        48%
        122 bp
        17.2
        400-24-Li41492-GCTTAACG_R1_kneaddata_paired_1
        18.8%
        49%
        113 bp
        11.7
        400-24-Li41492-GCTTAACG_R1_kneaddata_paired_2
        14.8%
        49%
        122 bp
        11.7
        500-01-Li41493-GTACCAAC_R1_kneaddata_paired_1
        18.3%
        48%
        113 bp
        2.8
        500-01-Li41493-GTACCAAC_R1_kneaddata_paired_2
        14.1%
        48%
        122 bp
        2.8
        500-02-Li41494-GAAGTCCT_R1_kneaddata_paired_1
        28.4%
        49%
        113 bp
        2.2
        500-02-Li41494-GAAGTCCT_R1_kneaddata_paired_2
        18.0%
        48%
        123 bp
        2.2
        500-03-Li41495-CCAATACG_R1_kneaddata_paired_1
        33.1%
        46%
        113 bp
        4.9
        500-03-Li41495-CCAATACG_R1_kneaddata_paired_2
        31.8%
        46%
        123 bp
        4.9
        500-04-Li41496-AGCTCTAG_R1_kneaddata_paired_1
        22.9%
        50%
        113 bp
        1.2
        500-04-Li41496-AGCTCTAG_R1_kneaddata_paired_2
        12.7%
        50%
        123 bp
        1.2
        500-06-Li41497-CGTAGCTA_R1_kneaddata_paired_1
        36.5%
        44%
        113 bp
        4.0
        500-06-Li41497-CGTAGCTA_R1_kneaddata_paired_2
        33.4%
        45%
        123 bp
        4.0
        500-07-Li41498-CTCTCACA_R1_kneaddata_paired_1
        25.9%
        47%
        113 bp
        5.9
        500-07-Li41498-CTCTCACA_R1_kneaddata_paired_2
        21.2%
        46%
        123 bp
        5.9
        500-08-Li41499-TGACCACA_R1_kneaddata_paired_1
        26.2%
        47%
        113 bp
        6.6
        500-08-Li41499-TGACCACA_R1_kneaddata_paired_2
        20.6%
        47%
        123 bp
        6.6
        500-09-Li41500-ATCCGGTA_R1_kneaddata_paired_1
        17.2%
        46%
        113 bp
        4.3
        500-09-Li41500-ATCCGGTA_R1_kneaddata_paired_2
        14.5%
        46%
        123 bp
        4.3
        500-10-Li41501-GACATCAC_R1_kneaddata_paired_1
        36.4%
        46%
        113 bp
        4.1
        500-10-Li41501-GACATCAC_R1_kneaddata_paired_2
        31.6%
        46%
        123 bp
        4.1
        500-11-Li41502-TCGATGGT_R1_kneaddata_paired_1
        21.0%
        46%
        112 bp
        2.3
        500-11-Li41502-TCGATGGT_R1_kneaddata_paired_2
        15.5%
        46%
        123 bp
        2.3
        500-12-Li41503-CTGTCAGA_R1_kneaddata_paired_1
        30.6%
        48%
        113 bp
        5.6
        500-12-Li41503-CTGTCAGA_R1_kneaddata_paired_2
        25.2%
        47%
        123 bp
        5.6
        500-13-Li41504-TGGTACGT_R1_kneaddata_paired_1
        21.2%
        44%
        113 bp
        2.3
        500-13-Li41504-TGGTACGT_R1_kneaddata_paired_2
        16.6%
        44%
        122 bp
        2.3
        500-14-Li41505-GATGCATC_R1_kneaddata_paired_1
        19.9%
        48%
        113 bp
        2.1
        500-14-Li41505-GATGCATC_R1_kneaddata_paired_2
        13.7%
        48%
        123 bp
        2.1
        500-15-Li41506-CTTCCAAC_R1_kneaddata_paired_1
        29.8%
        49%
        113 bp
        7.3
        500-15-Li41506-CTTCCAAC_R1_kneaddata_paired_2
        23.7%
        49%
        123 bp
        7.3
        500-16-Li41507-ACACGTGT_R1_kneaddata_paired_1
        19.5%
        46%
        113 bp
        4.3
        500-16-Li41507-ACACGTGT_R1_kneaddata_paired_2
        15.5%
        46%
        123 bp
        4.3
        500-17-Li41508-TAGGCCAT_R1_kneaddata_paired_1
        26.5%
        50%
        113 bp
        3.5
        500-17-Li41508-TAGGCCAT_R1_kneaddata_paired_2
        18.3%
        49%
        123 bp
        3.5
        500-18-Li41509-CTGTACAG_R1_kneaddata_paired_1
        17.6%
        50%
        113 bp
        1.5
        500-18-Li41509-CTGTACAG_R1_kneaddata_paired_2
        11.6%
        50%
        123 bp
        1.5
        500-19-Li41510-TCGAGTTG_R1_kneaddata_paired_1
        23.3%
        45%
        112 bp
        1.4
        500-19-Li41510-TCGAGTTG_R1_kneaddata_paired_2
        20.7%
        45%
        123 bp
        1.4
        500-20-Li41511-AAGGTTCC_R1_kneaddata_paired_1
        19.2%
        47%
        112 bp
        1.3
        500-20-Li41511-AAGGTTCC_R1_kneaddata_paired_2
        15.6%
        47%
        122 bp
        1.3
        500-21-Li41512-GCCGTATA_R1_kneaddata_paired_1
        12.2%
        47%
        113 bp
        2.7
        500-21-Li41512-GCCGTATA_R1_kneaddata_paired_2
        11.2%
        47%
        123 bp
        2.7
        500-22-Li41513-ACCTGTTC_R1_kneaddata_paired_1
        23.9%
        48%
        113 bp
        5.3
        500-22-Li41513-ACCTGTTC_R1_kneaddata_paired_2
        16.4%
        48%
        123 bp
        5.3
        500-23-Li41514-ACAGTCAC_R1_kneaddata_paired_1
        32.7%
        48%
        113 bp
        3.4
        500-23-Li41514-ACAGTCAC_R1_kneaddata_paired_2
        18.2%
        48%
        123 bp
        3.4
        500-24-Li41515-GAGTTCTG_R1_kneaddata_paired_1
        34.3%
        47%
        113 bp
        7.7
        500-24-Li41515-GAGTTCTG_R1_kneaddata_paired_2
        29.3%
        47%
        123 bp
        7.7
        500-25-Li41516-GCTACGAT_R1_kneaddata_paired_1
        29.5%
        50%
        113 bp
        8.4
        500-25-Li41516-GCTACGAT_R1_kneaddata_paired_2
        22.3%
        50%
        123 bp
        8.4
        500-26-Li41517-CTAGAGCT_R1_kneaddata_paired_1
        14.4%
        48%
        113 bp
        3.3
        500-26-Li41517-CTAGAGCT_R1_kneaddata_paired_2
        12.8%
        48%
        123 bp
        3.3
        500-27-Li41518-ACTGACTG_R1_kneaddata_paired_1
        25.0%
        48%
        113 bp
        4.1
        500-27-Li41518-ACTGACTG_R1_kneaddata_paired_2
        22.4%
        48%
        123 bp
        4.1
        500-28-Li41519-GGAAGCAT_R1_kneaddata_paired_1
        14.6%
        46%
        113 bp
        6.6
        500-28-Li41519-GGAAGCAT_R1_kneaddata_paired_2
        12.2%
        47%
        123 bp
        6.6
        500-29-Li41520-CCATATGG_R1_kneaddata_paired_1
        21.3%
        51%
        113 bp
        7.3
        500-29-Li41520-CCATATGG_R1_kneaddata_paired_2
        16.5%
        51%
        123 bp
        7.3
        500-30-Li41522-ACACGTCA_R1_kneaddata_paired_1
        16.9%
        47%
        113 bp
        6.3
        500-30-Li41522-ACACGTCA_R1_kneaddata_paired_2
        12.1%
        47%
        122 bp
        6.3
        500-31-Li41523-ACCAACGT_R1_kneaddata_paired_1
        37.6%
        48%
        113 bp
        7.9
        500-31-Li41523-ACCAACGT_R1_kneaddata_paired_2
        32.6%
        48%
        123 bp
        7.9
        500-32-Li41524-GATCAGCT_R1_kneaddata_paired_1
        24.2%
        49%
        113 bp
        10.3
        500-32-Li41524-GATCAGCT_R1_kneaddata_paired_2
        17.4%
        49%
        123 bp
        10.3
        500-33-Li41525-CGTAGCAT_R1_kneaddata_paired_1
        48.3%
        45%
        113 bp
        10.0
        500-33-Li41525-CGTAGCAT_R1_kneaddata_paired_2
        47.0%
        45%
        123 bp
        10.0
        500-34-Li41526-GTGTTGAC_R1_kneaddata_paired_1
        14.6%
        50%
        113 bp
        1.0
        500-34-Li41526-GTGTTGAC_R1_kneaddata_paired_2
        8.7%
        50%
        123 bp
        1.0
        500-35-Li41527-AGTGTCTG_R1_kneaddata_paired_1
        22.6%
        48%
        113 bp
        5.7
        500-35-Li41527-AGTGTCTG_R1_kneaddata_paired_2
        15.8%
        48%
        123 bp
        5.7
        500-36-Li41528-TGGTCATG_R1_kneaddata_paired_1
        29.6%
        53%
        114 bp
        6.3
        500-36-Li41528-TGGTCATG_R1_kneaddata_paired_2
        23.3%
        53%
        123 bp
        6.3
        500-37-Li41529-ACTGTGAC_R1_kneaddata_paired_1
        15.9%
        49%
        113 bp
        5.5
        500-37-Li41529-ACTGTGAC_R1_kneaddata_paired_2
        12.8%
        49%
        123 bp
        5.5
        500-38-Li41530-CTTGTCCA_R1_kneaddata_paired_1
        27.7%
        47%
        113 bp
        4.5
        500-38-Li41530-CTTGTCCA_R1_kneaddata_paired_2
        19.3%
        47%
        123 bp
        4.5
        500-39-Li41531-CGATCGAT_R1_kneaddata_paired_1
        29.4%
        50%
        113 bp
        11.9
        500-39-Li41531-CGATCGAT_R1_kneaddata_paired_2
        22.0%
        50%
        123 bp
        11.9
        500-40-Li41532-AACGTTGC_R1_kneaddata_paired_1
        36.2%
        48%
        113 bp
        7.8
        500-40-Li41532-AACGTTGC_R1_kneaddata_paired_2
        30.1%
        48%
        123 bp
        7.8
        500-41-Li41533-TGCACAAC_R1_kneaddata_paired_1
        27.2%
        47%
        113 bp
        6.5
        500-41-Li41533-TGCACAAC_R1_kneaddata_paired_2
        23.9%
        47%
        123 bp
        6.5
        500-42-Li41534-CTCTACAC_R1_kneaddata_paired_1
        8.1%
        45%
        113 bp
        1.8
        500-42-Li41534-CTCTACAC_R1_kneaddata_paired_2
        7.0%
        45%
        122 bp
        1.8
        500-43-Li41535-GCTATTCC_R1_kneaddata_paired_1
        24.7%
        50%
        113 bp
        5.3
        500-43-Li41535-GCTATTCC_R1_kneaddata_paired_2
        19.7%
        50%
        123 bp
        5.3
        500-44-Li41536-CCTAATCC_R1_kneaddata_paired_1
        26.6%
        47%
        113 bp
        3.4
        500-44-Li41536-CCTAATCC_R1_kneaddata_paired_2
        20.2%
        47%
        123 bp
        3.4
        500-45-Li41537-CATGCTTC_R1_kneaddata_paired_1
        31.4%
        46%
        113 bp
        7.1
        500-45-Li41537-CATGCTTC_R1_kneaddata_paired_2
        26.3%
        46%
        123 bp
        7.1
        500-46-Li41538-TGACGTGT_R1_kneaddata_paired_1
        34.6%
        47%
        113 bp
        9.7
        500-46-Li41538-TGACGTGT_R1_kneaddata_paired_2
        27.6%
        47%
        123 bp
        9.7
        500-47-Li41539-ACCACATG_R1_kneaddata_paired_1
        21.4%
        49%
        113 bp
        12.2
        500-47-Li41539-ACCACATG_R1_kneaddata_paired_2
        16.3%
        48%
        122 bp
        12.2
        500-48-Li41540-GACTTCAG_R1_kneaddata_paired_1
        26.4%
        51%
        114 bp
        8.4
        500-48-Li41540-GACTTCAG_R1_kneaddata_paired_2
        18.3%
        51%
        123 bp
        8.4
        500-49-Li41541-ACCAAGGA_R1_kneaddata_paired_1
        27.6%
        46%
        113 bp
        8.4
        500-49-Li41541-ACCAAGGA_R1_kneaddata_paired_2
        21.9%
        46%
        123 bp
        8.4
        500-50-Li41542-GCCGTTAA_R1_kneaddata_paired_1
        29.6%
        51%
        113 bp
        8.8
        500-50-Li41542-GCCGTTAA_R1_kneaddata_paired_2
        24.8%
        50%
        123 bp
        8.8
        500-51-Li41543-TGACTGAC_R1_kneaddata_paired_1
        12.2%
        48%
        113 bp
        3.6
        500-51-Li41543-TGACTGAC_R1_kneaddata_paired_2
        9.9%
        48%
        123 bp
        3.6
        500-52-Li41544-TGGTGTAC_R1_kneaddata_paired_1
        24.8%
        49%
        113 bp
        2.9
        500-52-Li41544-TGGTGTAC_R1_kneaddata_paired_2
        14.9%
        49%
        123 bp
        2.9
        500-53-Li41545-GTACAGCT_R1_kneaddata_paired_1
        36.0%
        51%
        113 bp
        5.0
        500-53-Li41545-GTACAGCT_R1_kneaddata_paired_2
        24.5%
        51%
        123 bp
        5.0
        500-54-Li41546-GGTTCCAA_R1_kneaddata_paired_1
        41.5%
        46%
        113 bp
        11.2
        500-54-Li41546-GGTTCCAA_R1_kneaddata_paired_2
        36.6%
        46%
        123 bp
        11.2
        500-55-Li41547-GAGACACA_R1_kneaddata_paired_1
        29.0%
        47%
        113 bp
        12.5
        500-55-Li41547-GAGACACA_R1_kneaddata_paired_2
        22.9%
        47%
        122 bp
        12.5
        500-56-Li41548-GAGTTCAC_R1_kneaddata_paired_1
        20.4%
        47%
        113 bp
        8.8
        500-56-Li41548-GAGTTCAC_R1_kneaddata_paired_2
        16.2%
        47%
        123 bp
        8.8
        500-57-Li41549-GCGCTATA_R1_kneaddata_paired_1
        15.0%
        47%
        113 bp
        5.8
        500-57-Li41549-GCGCTATA_R1_kneaddata_paired_2
        12.9%
        47%
        122 bp
        5.8
        500-58-Li41550-GTGAACAG_R1_kneaddata_paired_1
        18.5%
        48%
        113 bp
        3.7
        500-58-Li41550-GTGAACAG_R1_kneaddata_paired_2
        15.1%
        48%
        123 bp
        3.7
        500-59-Li41551-TGCACTAG_R1_kneaddata_paired_1
        19.9%
        47%
        113 bp
        5.2
        500-59-Li41551-TGCACTAG_R1_kneaddata_paired_2
        18.6%
        47%
        123 bp
        5.2
        500-60-Li41552-AACCGGTT_R1_kneaddata_paired_1
        24.8%
        47%
        113 bp
        8.0
        500-60-Li41552-AACCGGTT_R1_kneaddata_paired_2
        19.0%
        47%
        123 bp
        8.0
        500-61-Li41553-ATCCTAGG_R1_kneaddata_paired_1
        32.1%
        45%
        113 bp
        7.6
        500-61-Li41553-ATCCTAGG_R1_kneaddata_paired_2
        28.0%
        45%
        123 bp
        7.6
        500-62-Li41521-CAGTTGAC_R1_kneaddata_paired_1
        36.2%
        48%
        113 bp
        5.6
        500-62-Li41521-CAGTTGAC_R1_kneaddata_paired_2
        32.0%
        48%
        123 bp
        5.6
        BC-01-Li41556-GGATTAGG_R1_kneaddata_paired_1
        28.7%
        51%
        114 bp
        14.3
        BC-01-Li41556-GGATTAGG_R1_kneaddata_paired_2
        22.7%
        51%
        123 bp
        14.3
        BC-02-Li41557-GAACCATC_R1_kneaddata_paired_1
        28.8%
        50%
        113 bp
        11.9
        BC-02-Li41557-GAACCATC_R1_kneaddata_paired_2
        21.6%
        50%
        122 bp
        11.9
        BC-04-Li41559-GATCCTAG_R1_kneaddata_paired_1
        26.6%
        53%
        114 bp
        7.2
        BC-04-Li41559-GATCCTAG_R1_kneaddata_paired_2
        16.4%
        53%
        123 bp
        7.2
        BLANK-1-Li41554-CAACCTAG_R1_kneaddata_paired_1
        2.8%
        47%
        111 bp
        0.0
        BLANK-1-Li41554-CAACCTAG_R1_kneaddata_paired_2
        2.7%
        47%
        122 bp
        0.0
        BLANK-2-Li41555-AGTGGTCT_R1_kneaddata_paired_1
        3.0%
        46%
        111 bp
        0.0
        BLANK-2-Li41555-AGTGGTCT_R1_kneaddata_paired_2
        2.9%
        46%
        122 bp
        0.0
        PBS-Li41558-ATGCATGC_R1_kneaddata_paired_1
        38.5%
        52%
        113 bp
        12.6
        PBS-Li41558-ATGCATGC_R1_kneaddata_paired_2
        29.3%
        51%
        122 bp
        12.6

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        362 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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